Genome-wide identification, phylogeny, evolution, and expression patterns of MtN3/saliva/SWEET genes and functional analysis of BcNS in Brassica rapa

Abstract

BackgroundMembers of the MtN3/saliva/SWEET gene family are present in various organisms and are highly conserved. Their precise biochemical functions remain unclear, especially in Chinese cabbage. Based on the whole genome sequence, this study aims to identify the MtN3/saliva/SWEETs family members in Chinese cabbage and to analyze their classification, gene structure, chromosome distribution, phylogenetic relationship, expression pattern, and biological functions.ResultsWe identified 34 SWEET genes in Chinese cabbage and analyzed their localization on chromosomes and transmembrane regions of their corresponding proteins. Analysis of a phylogenetic tree indicated that there were at least 17 supposed ancestor genes before the separation in Brassica rapa and Arabidopsis. The expression patterns of these genes in different tissues and flower developmental stages of Chinese cabbage showed that they are mainly involved in reproductive development. The Ka/Ks ratio between paralogous SWEET gene pairs of B. rapa were far less than 1. In our previous study, At2g39060 homologous gene Bra000116 (BraSWEET9, also named BcNS, Brassica Nectary and Stamen) played an important role during flower development in Chinese cabbage. Instantaneous expression experiments in onion epidermal cells showed that the gene encoding this protein is localized to the plasma membrane. A basal nectary split is the phenotype of transgenic plants transformed with the antisense expression vector.ConclusionThis study is the first to perform a sequence analysis, structures analysis, physiological and biochemical characteristics analysis of the MtN3/saliva/SWEETs gene in Chinese cabbage and to verify the function of BcNS. A total of 34 SWEET genes were identified and they are distributed among ten chromosomes and one scaffold. The Ka/Ks ratio implies that the duplication genes suffered strong purifying selection for retention. These genes were differentially expressed in different floral organs. The phenotypes of the transgenic plants indicated that BcNs participates in the development of the floral nectary. This study provides a basis for further functional analysis of the MtN3/saliva/SWEETs gene family.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4554-8) contains supplementary material, which is available to authorized users.

Cysteine-Rich Receptor-Like Kinase Gene Family Identification in the Phaseolus Genome and Comparative Analysis of Their Expression Profiles Specific to Mycorrhizal and Rhizobial Symbiosis

“…The average of hydropathicity for the 46 CRKs was analyzed with ProtParam () utilizing the scoring criteria of Gasteiger et al [41]. The grand average of hydropathicity (GRAVY) value for the proteins was calculated as described by Miao et al [42].…”

The Expanded SWEET Gene Family Following Whole Genome Triplication in Brassica rapa

“…After that, 33 BrSWEET genes were identified from the B. rapa genome, and co-orthologs of SWEETs in A. thaliana were labeled by adding the sub-genome of the LF, MF1, or MF2 as a suffix (Figure 2A). Compared to the 34 SWEETs identified by Miao L et al [64], BrSWEET3-MF1 (gene ID: Bra029090) is not thought to belong to the BrSWEETs family, because of the absence of any of MTs or MtN3/PQ-loop and because it barely qualified for phylogenetic analysis. The distribution of SWEETs in A. thaliana and B. rapa on 24 GBs of ancestral crucifer karyotypes indicated that all of them are mapped on 14 of 24 GBs and they shared the same GBs for co-orthologous SWEETs (Figure 2A).…”

Comparative analysis of basic helix–loop–helix gene family among Brassica oleracea, Brassica rapa, and Brassica napus

“…With the rapid development of bioinformatics analysis, many genome sequences of Brassica plants have been completed at present [1,25,26]. Several gene families have been identified in Brassica to date [27][28][29]. After the discovery of bHLH motif with DNA binding and dimerization, increasing bHLH protein super families have been identified in plants and animals [4].…”